Thermoelectrics enable solid-state conversion of heat to electricity by the Seebeck effect, but must provide scalable and cost-effective technology for practical waste heat harvesting. This dissertation explores the thermoelectric properties of electrochemically etched silicon nanowires through experiments, complemented by charge and thermal transport theories. Electrolessly etched silicon nanowires show anomalously low thermal conductivity that has been attributed to the increased scattering of heat conducting phonons from the surface disorder introduced by etching. The reduction is below the incoherent limit for phonon scattering at the boundary, the so-called Casimir limit. A new model of partially coherent phonon transport shows that correlated multiple scattering of phonons off resonantly matched rough surfaces can indeed lead to thermal conductivity below the Casimir limit. Using design guidelines from the theory, silicon nanowires of controllable surface roughness are fabricated using metal-assisted chemical etching. Extensive characterization of the nanowire surfaces using transmission electron microscopy provides surface roughness parameters that are important in testing transport theories. The second part of the dissertation focuses on the implications of increased phonon scattering on the Seebeck coefficient, which is a cumulative effect of non-equilibrium amongst charge carriers and phonons. A novel frequency-domain technique enables simultaneous measurements of the Seebeck coefficient and the thermal conductivity of nanowire arrays. The frequency response measurements isolate the parasitic contributions thus improving upon existing techniques for cross-plane thermoelectric measurements. While the thermal conductivity of nanowires reduces significantly with increased roughness, there is also a significant reduction in the Seebeck coefficient over a wide range of doping. Theoretical fitting of the data reveals that such reduction results from the annihilation of phonon drag in nanowires due to phonon boundary scattering. By exploring the effect of surface roughness and employing lattice non-equilibrium theories, the measurements are able to distinguish between long wavelength phonons that contribute to phonon drag and shorter wavelengths that contribute to heat conduction near room temperature. Phonon drag quenching in nanostructures has implications beyond silicon and this thesis paves the way toward spectrally selective phonon scattering for improving nanoscale thermoelectrics.